Changelog

Unreleased

Fixes

  • Replaced stop-coordinate/C-terminal CDS matching with coordinate-normalised, strand- and phase-aware genomic overlap plus aligned translation comparison. Alternative starts, ambiguous X residues, small terminal differences, CDS-specific translation tables, codon_start, and missing translation qualifiers are now handled without unrestricted local matching.

Documentation

  • Audited repository documentation, public docstrings, CLI help, examples, and HPC templates against the current implementation.

  • Reconciled model identifiers with the live George Bouras Hugging Face namespace and documented current multitask versus deprecated 3Di-only models.

  • Documented 3Di and nullable 12-state output consistently, including the deterministic A–L serialisation.

  • Replaced automatic-normalisation guidance with raw JSON entropy and explicit downstream normalisation helpers.

  • Corrected coordinate, GenBank matching, ML splitting, missing-value, probability, device, and persistence descriptions.

  • Corrected the Read the Docs project name and aligned Python/tool version claims with package metadata and CI.

  • Made Sphinx warnings fatal in documentation CI and documented the local warnings-as-errors build command.

0.1.0 — 19 January 2026

Initial release with ORF discovery, translation, ProstT5 3Di encoding, raw Shannon entropy, modular CLI commands, JSON I/O, logging, batching, and device selection. Later releases added the unified schema, GenBank matching, ML, multi-GPU operation, and ModernProst/12-state support; those intermediate historical entries were not recorded in this file.